Y-12925842-CAG-C

Variant names:

• chrY-12925842-CAG-C
• rs16648

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.027 (0 hom., 908 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.053 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0265 AC: 905 AN: 34133 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00560

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0822

Gnomad EAS AF: 0.000782

Gnomad SAS AF: 0.0337

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.192

Gnomad NFE AF: 0.0331

Gnomad OTH AF: 0.0327

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0266 AC: 908 AN: 34198 Hom.: 0 Cov.: 0 AF XY: 0.0266 AC XY: 908 AN XY: 34198

African (AFR) AF: 0.00556 AC: 49 AN: 8808

American (AMR) AF: 0.0594 AC: 226 AN: 3805

Ashkenazi Jewish (ASJ) AF: 0.0822 AC: 64 AN: 779

East Asian (EAS) AF: 0.000782 AC: 1 AN: 1278

South Asian (SAS) AF: 0.0343 AC: 53 AN: 1546

European-Finnish (FIN) AF: 0.000283 AC: 1 AN: 3537

Middle Eastern (MID) AF: 0.194 AC: 14 AN: 72

European-Non Finnish (NFE) AF: 0.0332 AC: 454 AN: 13662

Other (OTH) AF: 0.0325 AC: 16 AN: 493

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.064

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs16648; hg19: chrY-15037754;